Package: adegenet 2.1.10

adegenet: Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Authors:Thibaut Jombart [aut], Zhian N. Kamvar [aut, cre], Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb], Lindsay V. Clark [ctb], Pavel Dimens [ctb]

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adegenet.pdf |adegenet.html
adegenet/json (API)

# Install adegenet in R:
install.packages('adegenet', repos = c('https://zkamvar.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thibautjombart/adegenet/issues

Datasets:
  • H3N2 - Seasonal influenza (H3N2) HA segment data
  • dapcIllus - Simulated data illustrating the DAPC
  • eHGDP - Extended HGDP-CEPH dataset
  • hybridtoy - Toy hybrid dataset
  • microbov - Microsatellites genotypes of 15 cattle breeds
  • nancycats - Microsatellites genotypes of 237 cats from 17 colonies of Nancy
  • rupica - Microsatellites genotypes of 335 chamois
  • sim2pop - Simulated genotypes of two georeferenced populations
  • spcaIllus - Simulated data illustrating the sPCA
  • swallowtails - Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada

On CRAN:

265 exports 165 stars 5.96 score 71 dependencies 26 dependents 13.1k downloads

Last updated 1 years agofrom:bb8b9e89674adf55993d7d5abc5995485b38b8c9

Exports:.genlab.internal_C_routines.readExt.render.server.info.rmspaces[.haploGena.scoreaddStrataaddStrata<-adegenetIssuesadegenetServeradegenetTutorialadegenetWebAIC.snapclustAICcAICc.snapclustalignment2genindallelesalleles<-any2colas.data.frame.genindas.data.frame.genlightas.data.frame.genpopas.genindas.genlightas.genpopas.genpop.genindas.igraph.haploGenas.igraph.seqTrackas.integer.SNPbinas.ktab.genindas.ktab.genpopas.ldaas.lda.dapcas.list.genlightas.matrixas.matrix.genindas.matrix.genlightas.matrix.genpopas.POSIXct.haploGenas.seqTrack.haploGenas.SNPbinassignplotazurBIC.snapclustbluepalbytesToBinIntbytesToIntc.SNPbincbind.genlightcbind.SNPbinCheckAllSegcheckTypechooseCNchrchr<-chromosomechromosome<-colorplotcolorplot.defaultcolorplot.spcacompoplotcompoplot.dapccompoplot.matrixcompoplot.snapclustcoords.monmoniercornerdapcdapc.data.framedapc.dudidapc.geninddapc.genlightdapc.matrixdeepseasundf2geninddist.genpopDNAbin2genindexport_to_mvmapperexport_to_mvmapper.dapcexport_to_mvmapper.defaultexport_to_mvmapper.dudiexport_to_mvmapper.spcaextract.PLINKmapfac2colfasta2DNAbinfasta2genlightfind.clustersfind.clusters.data.framefind.clusters.genindfind.clusters.genlightfind.clusters.matrixfindMutationsfindMutations.DNAbinflamefunkygengraphgengraph.defaultgengraph.distgengraph.DNAbingengraph.genindgengraph.genpopgengraph.matrixgenindgenind2dfgenind2genpopgenpopget.likelihoodget.likelihood.seqTrackglDotProdGLdotProdglMeanglNAglobal.rtestglPcaglPlotglSimglSumGLsumFreqGLsumIntglVargraphMutationsgraphMutations.DNAbingreenpalgreypalhaploGenhierhier<-HsHs.testHWE.test.genindhybridizehybridpalimport2genindinbreedingindNamesindNames<-initializeis.genindis.genpopisPolyKICKIC.snapclustlabels.haploGenlightseasunloadingplotloadingplot.defaultloadingplot.glPcalocal.rtestlocFaclocNameslocNames<-makefreqminorAllelemonmonierNA.posinAllnameStratanameStrata<-nb_shared_allnIndnLocnPopnum2colold2new_genindold2new_genlightold2new_genpopoptim.a.scoreoptimize.monmonierotherother<-pairDistpairDist.defaultpairDistPlotpairDistPlot.defaultpairDistPlot.distpairDistPlot.DNAbinpairDistPlot.genindpairDistPlot.matrixploidyploidy<-plotplot.haploGenplot.monmonierplot.seqTrackplot.spcaplotHaploGenplotSeqTrackpoppop<-popNamespopNames<-positionposition<-predict.dapcprint.dapcprint.genindSummaryprint.genpopSummaryprint.glPcaprint.haploGenprint.monmonierprint.spcapropSharedpropTypedrbind.genlightread.fstatread.genepopread.genetixread.PLINKread.snpread.structureredpalrepoolsample.haploGenscaleGenscatter.dapcscatter.glPcascreeplot.spcaseasunselPopSizeseplocseppopseqTrackseqTrack.defaultseqTrack.haploGenseqTrack.matrixsetPopsetPop<-showmekittenssnapclustsnapclust.choose.ksnpposi.plotsnpposi.plot.DNAbinsnpposi.plot.integersnpposi.plot.numericsnpposi.testsnpposi.test.DNAbinsnpposi.test.integersnpposi.test.numericsnpzipspcaspca_randtestspca.data.framespca.defaultspca.genindspca.genpopspca.matrixspectralsplitStratasplitStrata<-stratastrata<-summarysummary.dapcsummary.spcatabtransptruenamesviridwaspxvalDapcxvalDapc.data.framexvalDapc.defaultxvalDapc.genindxvalDapc.genlightxvalDapc.matrix

Dependencies:ade4apebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepermutepillarpixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vctrsveganviridisLitewithrxtable

Readme and manuals

Help Manual

Help pageTopics
Internal C routines.internal_C_routines binIntToBytes bytesToBinInt bytesToInt CheckAllSeg GLdotProd GLsumFreq GLsumInt nb_shared_all
Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)a.score optim.a.score
Accessors for adegenet objects$,genind-method $,genpop-method $<-,genind-method $<-,genpop-method alleles alleles,gen-method alleles,genind-method alleles,genpop-method alleles<- alleles<-,gen-method alleles<-,genind-method alleles<-,genpop-method indNames indNames,genind-method indNames<- indNames<-,genind-method locFac locFac,gen-method locFac,genind-method locFac,genpop-method locNames locNames,gen-method locNames,genind-method locNames,genpop-method locNames<- locNames<-,gen-method locNames<-,genind-method locNames<-,genpop-method nAll nAll,gen-method nAll,genind-method nAll,genpop-method nInd nInd,genind-method nLoc nLoc,gen-method nLoc,genind-method nLoc,genpop-method nPop nPop,genind-method nPop,genpop-method other other,gen-method other,genind-method other,genpop-method other<- other<-,gen-method other<-,genind-method other<-,genpop-method ploidy ploidy,genind-method ploidy,genpop-method ploidy<- ploidy<-,genind-method ploidy<-,genpop-method pop pop,genind-method pop<- pop<-,gen-method pop<-,genind-method popNames popNames,genind-method popNames,genpop-method popNames<- popNames<-,genind-method popNames<-,genpop-method [,genind,ANY,ANY,ANY-method [,genind-method [,genpop,ANY,ANY,ANY-method [,genpop-method
Web servers for adegenetadegenetServer
The adegenet packageadegenet adegenet.package
Functions to access online resources for adegenetadegenetIssues adegenetTutorial adegenetWeb
Compute Akaike Information Criterion (AIC) for snapclustAIC.snapclust
Compute Akaike Information Criterion for small samples (AICc) for snapclustAICc AICc.snapclust
Converting genind/genpop objects to other classesas,genind,data.frame-method as,genind,genpop-method as,genind,ktab-method as,genind,matrix-method as,genpop,data.frame-method as,genpop,ktab-method as,genpop,matrix-method as-method as.data.frame.genind as.data.frame.genpop as.genpop.genind as.ktab.genind as.ktab.genpop as.matrix.genind as.matrix.genpop coerce,genind,data.frame-method coerce,genind,genpop-method coerce,genind,ktab-method coerce,genind,matrix-method coerce,genpop,data.frame-method coerce,genpop,ktab-method coerce,genpop,matrix-method ktab-class
Conversion to class "genlight"as,genlight,data.frame-method as,genlight,list-method as,genlight,matrix-method as.genlight as.genlight,data.frame-method as.genlight,list-method as.genlight,matrix-method coerce,genlight,data.frame-method coerce,genlight,list-method coerce,genlight,matrix-method
Conversion to class "SNPbin"as,SNPbin,integer-method as,SNPbin,numeric-method as.SNPbin as.SNPbin,integer-method as.SNPbin,numeric-method coerce,integer,SNPbin-method coerce,numeric,SNPbin-method
Auxiliary functions for adegenet.genlab .readExt .rmspaces any2col azur bluepal checkType corner deepseasun fac2col flame funky greenpal greypal hybridpal lightseasun num2col redpal seasun spectral transp virid wasp
Compute Bayesian Information Criterion (BIC) for snapclustBIC.snapclust
Function to choose a connection networkchooseCN
Represents a cloud of points with colorscolorplot colorplot.default
Genotype composition plotcompoplot compoplot.dapc compoplot.matrix compoplot.snapclust
Returns original points in results paths of an object of class 'monmonier'coords.monmonier
Discriminant Analysis of Principal Components (DAPC)as.lda as.lda.dapc dapc dapc.data.frame dapc.dudi dapc.genind dapc.genlight dapc.matrix predict.dapc print.dapc summary.dapc
Cross-validation for Discriminant Analysis of Principal Components (DAPC)xvalDapc xvalDapc.data.frame xvalDapc.default xvalDapc.genind xvalDapc.genlight xvalDapc.matrix
Graphics for Discriminant Analysis of Principal Components (DAPC)assignplot scatter.dapc
Simulated data illustrating the DAPCdapcIllus
Convert a data.frame of allele data to a genind object.df2genind
Genetic distances between populationsdist.genpop
Extended HGDP-CEPH dataseteHGDP
Export analysis for mvmapper visualisationexport_to_mvmapper export_to_mvmapper.dapc export_to_mvmapper.default export_to_mvmapper.dudi export_to_mvmapper.spca
Reading PLINK Single Nucleotide Polymorphism dataextract.PLINKmap read.PLINK read.plink
Read large DNA alignments into Rfasta2DNAbin
Extract Single Nucleotide Polymorphism (SNPs) from alignmentsfasta2genlight
find.cluster: cluster identification using successive K-means.find.sub.clusters find.clusters find.clusters.data.frame find.clusters.genind find.clusters.genlight find.clusters.matrix
Identify mutations between DNA sequencesfindMutations findMutations.DNAbin graphMutations graphMutations.DNAbin
Genetic transitive graphsgengraph gengraph.default gengraph.dist gengraph.DNAbin gengraph.genind gengraph.genpop gengraph.matrix
adegenet formal class (S4) for individual genotypes.valid.genind genind-class is.genind names,genind-method print,genind-method print,genindSummary-method print.genindSummary show,genind-method summary,genind-method
Convert a genind object to a data.frame.genind2df
Conversion from a genind to a genpop objectgenind2genpop
Auxiliary functions for genlight objectsglDotProd glMean glNA glSum glVar
Formal class "genlight"$,genlight-method $<-,genlight-method alleles,genlight-method alleles<-,genlight-method as,data.frame,genlight-method as,list,genlight-method as,matrix,genlight-method as.data.frame.genlight as.list.genlight as.matrix.genlight cbind.genlight chr chr,genlight-method chr<- chr<-,genlight-method chromosome chromosome,genlight-method chromosome<- chromosome<-,genlight-method coerce,data.frame,genlight-method coerce,list,genlight-method coerce,matrix,genlight-method dim,genlight-method genlight genlight-class indNames,genlight-method indNames<-,genlight-method initialize,genlight-method locNames,genlight-method locNames<-,genlight-method NA.posi NA.posi,genlight-method names,genlight-method nInd,genlight-method nLoc,genlight-method nPop,genlight-method other,genlight-method other<-,genlight-method ploidy,genlight-method ploidy<-,genlight-method pop,genlight-method pop<-,genlight-method popNames,genlight-method popNames<-,genlight-method position position,genlight-method position<- position<-,genlight-method rbind.genlight show,genlight-method tab,genlight-method [,genlight,ANY,ANY,ANY-method [,genlight,ANY,ANY-method [,genlight-method
adegenet formal class (S4) for allele counts in populationsdist,genpop,ANY,ANY,ANY,missing-method genpop-class is.genpop names,genpop-method print,genpopSummary-method print.genpopSummary show,genpop-method summary,genpop-method
Global and local testsglobal.rtest local.rtest
Principal Component Analysis for genlight objectsglPca loadingplot.glPca print.glPca scatter.glPca
Plotting genlight objectsglPlot plot,genlight,ANY-method plot,genlight-method plot.genlight
Simulation of simple genlight objectsglSim
Seasonal influenza (H3N2) HA segment dataH3N2 USflu usflu USflu.fasta usflu.fasta
Simulation of genealogies of haplotypesas.igraph.haploGen as.POSIXct.haploGen as.seqTrack.haploGen haploGen haploGen-class labels.haploGen plot.haploGen plotHaploGen print.haploGen sample.haploGen seqTrack.haploGen [.haploGen
Access and manipulate the population hierarchy for genind or genlight objects.hier hier,genind-method hier,genlight-method hier<- hier<-,genind-method hier<-,genlight-method
Expected heterozygosity (Hs)Hs
Test differences in expected heterozygosity (Hs)Hs.test
Hardy-Weinberg Equilibrium test for multilocus dataHWE.test.genind
Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.hybridize
Toy hybrid datasethybridtoy
Importing data from several softwares to a genind objectimport2genind
Likelihood-based estimation of inbreedinginbreeding
genind constructoras.genind genind initialize,genind-method initialize,genind-methods
genpop constructoras.genpop genpop initialize,genpop-method initialize,genpop-methods
Assess polymorphism in genind/genpop objectsisPoly isPoly,genind-method isPoly,genpop-method isPoly-methods
Compute Akaike Information Criterion for small samples (AICc) for snapclustKIC KIC.snapclust
Represents a cloud of points with colorsloadingplot loadingplot.default
Compute allelic frequenciesmakefreq makefreq,genind-method makefreq,genind-methods makefreq,genpop-method makefreq,genpop-methods makefreq.genind makefreq.genpop
Microsatellites genotypes of 15 cattle breedsmicrobov
Compute minor allele frequencyminorAllele
Boundary detection using Monmonier algorithmmonmonier optimize.monmonier plot.monmonier print.monmonier
Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)nancycats
Convert objects with obsolete classes into new objectsold2new old2new_genind old2new_genlight old2new_genpop
Pairwise distance plotspairDist pairDist.default pairDistPlot pairDistPlot.default pairDistPlot.dist pairDistPlot.DNAbin pairDistPlot.genind pairDistPlot.matrix
Compute proportion of shared allelespropShared
Compute the proportion of typed elementspropTyped propTyped,genind-method propTyped,genpop-method propTyped-methods
Reading data from Fstatread.fstat
Reading data from Genepopread.genepop
Reading data from GENETIXread.genetix
Reading Single Nucleotide Polymorphism dataread.snp
Reading data from STRUCTUREread.structure
Pool several genotypes into a single datasetrepool
Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)rupica
Compute scaled allele frequenciesscaleGen scaleGen,genind-method scaleGen,genpop-method scaleGen-methods
Select genotypes of well-represented populationsselPopSize selPopSize,ANY-method selPopSize,genind-method selPopSize-methods
Separate data per locusseploc seploc,ANY-method seploc,genind-method seploc,genlight-method seploc,genpop-method seploc-methods
Separate genotypes per populationseppop seppop,ANY-method seppop,genind-method seppop,genlight-method seppop-methods
SeqTrack algorithm for reconstructing genealogiesas.igraph.seqTrack get.likelihood get.likelihood.seqTrack plot.seqTrack plotSeqTrack seqTrack seqTrack-class seqTrack.default seqTrack.matrix
Importing data from an alignement of sequences to a genind objectalignment2genind DNAbin2genind
Manipulate the population factor of genind objects.setPop setPop,genind-method setPop,genlight-method setPop<- setPop<-,genind-method setPop<-,genlight-method
When you need a break...showmekittens
Simulated genotypes of two georeferenced populationssim2pop
Maximum-likelihood genetic clustering using EM algorithmsnapclust
Choose the number of clusters for snapclust using AIC, BIC or AICcsnapclust.choose.k
Formal class "SNPbin"$,SNPbin-method $<-,SNPbin-method as,integer,SNPbin-method as,numeric,SNPbin-method as.integer.SNPbin c.SNPbin cbind.SNPbin coerce,SNPbin,integer-method initialize,SNPbin-method NA.posi,SNPbin-method names,SNPbin-method nLoc,SNPbin-method ploidy,SNPbin-method ploidy<-,SNPbin-method show,SNPbin-method SNPbin SNPbin-class [,SNPbin,ANY,ANY,ANY-method [,SNPbin,ANY,ANY-method [,SNPbin-method
Analyse the position of polymorphic sitessnpposi.plot snpposi.plot.DNAbin snpposi.plot.integer snpposi.plot.numeric snpposi.test snpposi.test.DNAbin snpposi.test.integer snpposi.test.numeric
Identification of structural SNPssnpzip
Spatial principal component analysiscolorplot.spca plot.spca print.spca screeplot.spca spca spca.data.frame spca.default spca.genind spca.genpop spca.matrix summary.spca
Monte Carlo test for sPCAspca_randtest
Simulated data illustrating the sPCAspcaIllus
Access and manipulate the population strata for genind or genlight objects.addStrata addStrata,genind-method addStrata,genlight-method addStrata<- addStrata<-,genind-method addStrata<-,genlight-method nameStrata nameStrata,genind-method nameStrata,genlight-method nameStrata<- nameStrata<-,genind-method nameStrata<-,genlight-method splitStrata splitStrata,genind-method splitStrata,genlight-method splitStrata<- splitStrata<-,genind-method splitStrata<-,genlight-method strata strata,genind-method strata,genlight-method strata<- strata<-,genind-method strata<-,genlight-method
Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canadaswallowtails
Access allele counts or frequenciestab tab,genind-method tab,genind-methods tab,genpop-method tab,genpop-methods tab.genind tab.genpop
Restore true labels of an objecttruenames truenames,ANY-method truenames,genind-method truenames,genpop-method truenames-methods
Virtual classes for adegenetcallOrNULL-class charOrNULL-class dfOrNULL-class factorOrNULL-class formOrNULL-class gen-class indInfo-class intOrNULL-class intOrNum-class listOrNULL-class popInfo-class